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Thomas T. Perkins

TitleProfessor Adjoint
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction
Phone303/492-5291

    Collapse Research 
    Collapse research activities and funding
    R01HL117138     (LEINWAND, LESLIE ANNE)Aug 20, 2013 - Jan 31, 2022
    NIH
    Molecular characterization of cardiomyopathy mutations in human cardiac myosin
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods Mol Biol. 2022; 2478:273-312. PMID: 36063324.
      View in: PubMed
    2. Jacobson DR, Perkins TT. Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy. Proc Natl Acad Sci U S A. 2021 03 30; 118(13). PMID: 33753487.
      View in: PubMed
    3. Edwards DT, LeBlanc MA, Perkins TT. Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations. Proc Natl Acad Sci U S A. 2021 03 23; 118(12). PMID: 33723041.
      View in: PubMed
    4. LeBlanc MA, Fink MR, Perkins TT, Sousa MC. Type III secretion system effector proteins are mechanically labile. Proc Natl Acad Sci U S A. 2021 03 23; 118(12). PMID: 33723050.
      View in: PubMed
    5. Yu H, Jacobson DR, Luo H, Perkins TT. Quantifying the Native Energetics Stabilizing Bacteriorhodopsin by Single-Molecule Force Spectroscopy. Phys Rev Lett. 2020 Aug 07; 125(6):068102. PMID: 32845671.
      View in: PubMed
    6. Jacobson DR, Perkins TT. Correcting molecular transition rates measured by single-molecule force spectroscopy for limited temporal resolution. Phys Rev E. 2020 Aug; 102(2-1):022402. PMID: 32942397.
      View in: PubMed
    7. Heenan PR, Wang X, Gooding AR, Cech TR, Perkins TT. Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid. Nucleic Acids Res. 2020 04 06; 48(6):2969-2981. PMID: 32043141.
      View in: PubMed
    8. Jacobson DR, Uyetake L, Perkins TT. Membrane-Protein Unfolding Intermediates Detected with Enhanced Precision Using a Zigzag Force Ramp. Biophys J. 2020 02 04; 118(3):667-675. PMID: 31882249.
      View in: PubMed
    9. Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS Nano. 2019 04 23; 13(4):4220-4229. PMID: 30938988.
      View in: PubMed
    10. Yu H, Heenan PR, Edwards DT, Uyetake L, Perkins TT. Quantifying the Initial Unfolding of Bacteriorhodopsin Reveals Retinal Stabilization. Angew Chem Int Ed Engl. 2019 02 04; 58(6):1710-1713. PMID: 30556941.
      View in: PubMed
    11. Walder R, Van Patten WJ, Ritchie DB, Montange RK, Miller TW, Woodside MT, Perkins TT. High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy. Nano Lett. 2018 10 10; 18(10):6318-6325. PMID: 30234311.
      View in: PubMed
    12. Heenan PR, Perkins TT. FEATHER: Automated Analysis of Force Spectroscopy Unbinding and Unfolding Data via?a?Bayesian Algorithm. Biophys J. 2018 09 04; 115(5):757-762. PMID: 30122292.
      View in: PubMed
    13. Heenan PR, Yu H, Siewny MGW, Perkins TT. Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy. J Chem Phys. 2018 Mar 28; 148(12):123313. PMID: 29604885.
      View in: PubMed
    14. Lopes FB, Wu XL, Li H, Xu J, Perkins T, Genho J, Ferretti R, Tait RG, Bauck S, Rosa GJM. Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes. J Anim Breed Genet. 2018 Feb; 135(1):14-27. PMID: 29345073.
      View in: PubMed
    15. Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS Nano. 2018 01 23; 12(1):198-207. PMID: 29244486.
      View in: PubMed
    16. Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem. 2018 01 05; 19(1):19-23. PMID: 29069529.
      View in: PubMed
    17. Edwards DT, Faulk JK, LeBlanc MA, Perkins TT. Force Spectroscopy with 9-?s Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry. Biophys J. 2017 Dec 19; 113(12):2595-2600. PMID: 29132641.
      View in: PubMed
    18. Okoniewski SR, Uyetake L, Perkins TT. Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA. Nucleic Acids Res. 2017 Oct 13; 45(18):10775-10782. PMID: 28977580.
      View in: PubMed
    19. Walder R, LeBlanc MA, Van Patten WJ, Edwards DT, Greenberg JA, Adhikari A, Okoniewski SR, Sullan RMA, Rabuka D, Sousa MC, Perkins TT. Rapid Characterization of a Mechanically Labile a-Helical Protein Enabled by Efficient Site-Specific Bioconjugation. J Am Chem Soc. 2017 07 26; 139(29):9867-9875. PMID: 28677396.
      View in: PubMed
    20. Yu H, Siewny MG, Edwards DT, Sanders AW, Perkins TT. Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. Science. 2017 Mar 03; 355(6328):945-950. PMID: 28254940.
      View in: PubMed
    21. Okoniewski SR, Carter AR, Perkins TT. A Surface-Coupled Optical Trap with 1-bp Precision via Active Stabilization. Methods Mol Biol. 2017; 1486:77-107. PMID: 27844426.
      View in: PubMed
    22. Faulk JK, Edwards DT, Bull MS, Perkins TT. Improved Force Spectroscopy Using Focused-Ion-Beam-Modified Cantilevers. Methods Enzymol. 2017; 582:321-351. PMID: 28062041.
      View in: PubMed
    23. Carter AR, Seaberg MH, Fan HF, Sun G, Wilds CJ, Li HW, Perkins TT. Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD-DNA complexes. Nucleic Acids Res. 2016 07 08; 44(12):5849-60. PMID: 27220465.
      View in: PubMed
    24. Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution. J Struct Biol. 2017 01; 197(1):13-25. PMID: 26804584.
      View in: PubMed
    25. Edwards DT, Faulk JK, Sanders AW, Bull MS, Walder R, LeBlanc MA, Sousa MC, Perkins TT. Optimizing 1-?s-Resolution Single-Molecule Force Spectroscopy on a Commercial Atomic Force Microscope. Nano Lett. 2015 Oct 14; 15(10):7091-8. PMID: 26421945.
      View in: PubMed
    26. He C, Hu C, Hu X, Hu X, Xiao A, Perkins TT, Li H. Direct Observation of the Reversible Two-State Unfolding and Refolding of an a/? Protein by Single-Molecule Atomic Force Microscopy. Angew Chem Int Ed Engl. 2015 Aug 17; 54(34):9921-5. PMID: 26136291.
      View in: PubMed
    27. Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. Opt Express. 2015 Jun 29; 23(13):16554-64. PMID: 26191667.
      View in: PubMed
    28. Churnside AB, Perkins TT. Ultrastable atomic force microscopy: improved force and positional stability. FEBS Lett. 2014 Oct 01; 588(19):3621-30. PMID: 24801176.
      View in: PubMed
    29. Bull MS, Sullan RM, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. ACS Nano. 2014 May 27; 8(5):4984-95. PMID: 24670198.
      View in: PubMed
    30. Perkins TT. ?ngstr?m-precision optical traps and applications. Annu Rev Biophys. 2014; 43:279-302. PMID: 24773015.
      View in: PubMed
    31. Berweger S, Nguyen DM, Muller EA, Bechtel HA, Perkins TT, Raschke MB. Nano-chemical infrared imaging of membrane proteins in lipid bilayers. J Am Chem Soc. 2013 Dec 11; 135(49):18292-5. PMID: 24251914.
      View in: PubMed
    32. Paik DH, Roskens VA, Perkins TT. Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method. Nucleic Acids Res. 2013 Oct; 41(19):e179. PMID: 23935118.
      View in: PubMed
    33. Sullan RM, Churnside AB, Nguyen DM, Bull MS, Perkins TT. Atomic force microscopy with sub-picoNewton force stability for biological applications. Methods. 2013 Apr 01; 60(2):131-41. PMID: 23562681.
      View in: PubMed
    34. Montange RK, Bull MS, Shanblatt ER, Perkins TT. Optimizing bead size reduces errors in force measurements in optical traps. Opt Express. 2013 Jan 14; 21(1):39-48. PMID: 23388894.
      View in: PubMed
    35. Churnside AB, Sullan RM, Nguyen DM, Case SO, Bull MS, King GM, Perkins TT. Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy. Nano Lett. 2012 Jul 11; 12(7):3557-61. PMID: 22694769.
      View in: PubMed
    36. Paik DH, Perkins TT. Single-molecule optical-trapping measurements with DNA anchored to an array of gold nanoposts. Methods Mol Biol. 2012; 875:335-56. PMID: 22573450.
      View in: PubMed
    37. Paik DH, Perkins TT. Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy. Angew Chem Int Ed Engl. 2012 Feb 20; 51(8):1811-5. PMID: 22162006.
      View in: PubMed
    38. Paik DH, Perkins TT. Overstretching DNA at 65 pN does not require peeling from free ends or nicks. J Am Chem Soc. 2011 Mar 16; 133(10):3219-21. PMID: 21207940.
      View in: PubMed
    39. Churnside AB, King GM, Perkins TT. Label-free optical imaging of membrane patches for atomic force microscopy. Opt Express. 2010 Nov 08; 18(23):23924-32. PMID: 21164738.
      View in: PubMed
    40. Perkins TT, Li HW. Single-molecule studies of RecBCD. Methods Mol Biol. 2010; 587:155-72. PMID: 20225148.
      View in: PubMed
    41. Paik DH, Seol Y, Halsey WA, Perkins TT. Integrating a high-force optical trap with gold nanoposts and a robust gold-DNA bond. Nano Lett. 2009 Aug; 9(8):2978-83. PMID: 19492836.
      View in: PubMed
    42. Carter AR, Seol Y, Perkins TT. Precision surface-coupled optical-trapping assay with one-basepair resolution. Biophys J. 2009 Apr 08; 96(7):2926-34. PMID: 19348774.
      View in: PubMed
    43. King GM, Carter AR, Churnside AB, Eberle LS, Perkins TT. Ultrastable atomic force microscopy: atomic-scale stability and registration in ambient conditions. Nano Lett. 2009 Apr; 9(4):1451-6. PMID: 19351191.
      View in: PubMed
    44. Carter AR, King GM, Perkins TT. Back-scattered detection provides atomic-scale localization precision, stability, and registration in 3D. Opt Express. 2007 Oct 01; 15(20):13434-45. PMID: 19550612.
      View in: PubMed
    45. Seol Y, Li J, Nelson PC, Perkins TT, Betterton MD. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. Biophys J. 2007 Dec 15; 93(12):4360-73. PMID: 17766363.
      View in: PubMed
    46. Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, Goodrich JA. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J Mol Biol. 2007 Sep 21; 372(3):619-32. PMID: 17681538.
      View in: PubMed
    47. Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT. Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl Opt. 2007 Jan 20; 46(3):421-7. PMID: 17228390.
      View in: PubMed
    48. Seol Y, Carpenter AE, Perkins TT. Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating. Opt Lett. 2006 Aug 15; 31(16):2429-31. PMID: 16880845.
      View in: PubMed
    49. Nugent-Glandorf L, Perkins TT. Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection. Opt Lett. 2004 Nov 15; 29(22):2611-3. PMID: 15552661.
      View in: PubMed
    50. Perkins TT, Li HW, Dalal RV, Gelles J, Block SM. Forward and reverse motion of single RecBCD molecules on DNA. Biophys J. 2004 Mar; 86(3):1640-8. PMID: 14990491.
      View in: PubMed
    51. Perkins TT, Dalal RV, Mitsis PG, Block SM. Sequence-dependent pausing of single lambda exonuclease molecules. Science. 2003 Sep 26; 301(5641):1914-8. PMID: 12947034.
      View in: PubMed
    52. Perkins TT, Smith DE, Chu S. Single polymer dynamics in an elongational flow. Science. 1997 Jun 27; 276(5321):2016-21. PMID: 9197259.
      View in: PubMed
    53. Perkins TT, Smith DE, Larson RG, Chu S. Stretching of a single tethered polymer in a uniform flow. Science. 1995 Apr 07; 268(5207):83-7. PMID: 7701345.
      View in: PubMed
    54. Perkins TT, Quake SR, Smith DE, Chu S. Relaxation of a single DNA molecule observed by optical microscopy. Science. 1994 May 06; 264(5160):822-6. PMID: 8171336.
      View in: PubMed
    55. Perkins TT, Smith DE, Chu S. Direct observation of tube-like motion of a single polymer chain. Science. 1994 May 06; 264(5160):819-22. PMID: 8171335.
      View in: PubMed
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